Characterization of antimicrobial resistance genes and class 1 integrase gene in raw meat and aquatic product, fresh vegetable and fruit, and swine manure in southern China

Abstract

Various antimicrobial resistance (AMR) genes, especially a widely diverse assembly of mobile genetic elements such as plasmids, integrons, gene cassettes, or transposons, recently identified environmental pollutants, have been widely recognized as one of the main global health concerns, threatening food safety, and human and animal health. In order to determine the contamination of AMR genes and class 1 integrase gene (intI1) in raw or fresh food and swine manure in southern China, 119 samples of raw or fresh foods were investigated (raw meat and aquatic product, fresh vegetables and fruits) and 10 samples of swine manures from Guangzhou and Xiamen were analyzed for the prevalence and distribution of 11 AMR genes and intI1 using real-time PCR. The 11 AMR genes belonged to tetracycline (tetA, tetB, tetM), aminoglycoside (aadA, aphA-1), sulfonamide (sulI, sulII), chloromycetin (cmlA, floR), erythromycin (ermB), and disinfectant resistance genes (qacE). TetA was the most frequently detected gene in food samples, with a frequency of 100% in all samples. The detection frequencies of aadA, aph-1, floR, sulI, intI1, qacE, sulII, tetB, and tetM in food samples were above 90%, whereas cmlA and ermB had lower detection frequencies (89.9% and 84.0%, respectively). Tetracycline and aminoglycoside resistance genes were the most prevalent genes in food samples, with an average abundance of 3.08 and 1.18 copies/16S rRNA gene copy, respectively. Principal component analysis revealed that the comprehensive contamination of AMR genes in aquatic products was different from that of agricultural products. IntI1 of class 1 integron, and its most commonly contain resistance cassettes encoding aadA genes, as well as cmlA, qacE, sulI, and sulII genes, were present in significantly lower abundance in aquatic than agricultural products. Dominant AMR genes in swine manure samples were tetM, qacE, aadA, and cmlA, with an average abundance above 107copies/g. The high prevalence of AMR genes and intI1 in raw or fresh food highlighted the roles of raw or fresh foods as potential sources for antimicrobial resistance genes and raised the need for controlling AMR genes transmission through the food chain.